The game consists of several campaigns for each one of ten world areas. The campaigns are themed around real events or activities in these areas (e.g. escorting a UN humanitarian convoy during the Bosnian War, fighting pirates in the South China Sea, etc.)
A typical campaign consists of four or five missions. Each mission has a primary objective that must be completed to successfully complete the mission, there are other targets in each missions such as tanks and SAM launchers but these are only used to help the player boost their score. The primary target is usually a major structure like an enemy base or a bridge.
Usually the player is equipped with a standard set of weapons - 16 missiles, 76 rockets, and a machine gun with unlimited ammunition. On some special missions the rockets are replaced by a weapon that is critical to the success of that particular mission, such as a runway cratering system when the primary objective is to destroy an airbase or a bomb when destruction of a bridge is the primary objective.
The control system for Thunderhawk was fairly unusual for the platforms supporting a mouse. It used the mouse for basic control, plus some keyboard input for rarely used commands. Moving the mouse would tilt the helicopter in the specified direction, and make it start moving in that direction. Pressing the left mouse button fires weapons. When the right mouse button was held, moving the mouse up and down changed altitude, while side to side yawed the helicopter side to side.